I had something with this years ago.... someone gave me a script to build a
protein aggregate which, cut'n'pasted into xleap, built a system with
L-amino acids, but run from tleap built a system made of equal parts L & D
amino acids. Guess which one ended up getting run!
Stupid to have an odd number of reflections in your leap script.... but
then again, if it looks ok in xleap then it *is* ok, right?
If anyone asked me then I would say that the correct behaviour should be to
allow creation of stereoisomers (tleap behaviour), rather than forbidding
it (xleap behaviour)...but as long as they are consistent then either way
should be OK.
Sadly, I've lost the original script with this fascinating behaviour but it
sounds like Lachele can reproduce something similar. The gist of it was
just to have an odd number of reflection operations.
Josh
On 17 November 2011 17:35, B. Lachele Foley <lfoley.uga.edu> wrote:
> Ah... chirality. This is an old issue in tleap, and it doesn't only
> affect higher coordination numbers. I'm trying to remember if/when/how any
> of us said anything about it. I fear that by the time we found
> workarounds, the combined effects of exhaustion, frustration and
> anticipation of another hour or two to generate a coherent bug report
> resulted in forgetting entirely to mention it to anyone else.
>
> We always have to double-check our structures to be sure an alpha sugar
> has not suddenly been made beta. This occurs in some situations when using
> the sequence command. I think sleap did this too, but can't be sure. I
> can provide an example, if desired. The workaround... oh... I think
> involved very careful fragmenting and ordering when building the structures
> and in setting heads and tails much more often than should be necessary.
>
> Another puzzling behavior is that the copy command will invert chirality
> (anomeric center only, as I recall) in certain cases. The fix to this was
> simple -- copy twice.
>
> In a possibly related bug... we have found that in some situations, a
> subsequent impose command will be applied to all previous impose's.
>
> Sorry I don't know the code involved in that, and I don't think any of the
> rest around here do, but these semi-related behaviors might help find the
> trouble.
>
> :-) Lachele
>
> Dr. B. Lachele Foley
> Complex Carbohydrate Research Center
> The University of Georgia
> Athens, GA USA
> lfoley.uga.edu
> http://glycam.ccrc.uga.edu
>
> ________________________________________
> From: Mark Williamson [mjw.mjw.name]
> Sent: Thursday, November 17, 2011 11:13 AM
> To: AMBER Developers Mailing List
> Subject: [AMBER-Developers] Chirality routines in tleap; do they do the
> correct thing with coordination numbers >4
>
> Dear All,
>
> I'm currently hitting an issue within tleap when loading a PDB file
> corresponding to a predefined residue. Specifically, it is being
> triggered when tleap adds a missing heaving atom which is absent the
> PDB. The reside is a heme residue in the compound I state and the PDB is
> missing the ferryl oxygen (O1).
>
> I've entered this in AMBER's bugzilla with lots more information and a
> test case:
>
> http://bugzilla.ambermd.org/show_bug.cgi?id=151
>
> I'd be really grateful if someone more familiar with this code could
> perhaps suggest some new ideas for me to try with respect to this.
>
> Thanks,
>
> Mark
>
> _______________________________________________
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>
>
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Received on Fri Nov 18 2011 - 01:00:04 PST
